Novel approach for segmentation of brain magnetic

resonance imaging using intensity based thresholding

D.Selvaraj
Dept. of Electronics and Communication Engineering
Sathyabama University
Chennai, India
mailsselvaraj!yahoo.com
".Dhanase#aran
Dept. of Electrical and Electronics Engineering
Syed $mmal Engineering College
"amanathapuram, India
rdhanashe#ar!yahoo.com
AbstractMagnetic resonance imaging (MRI) is an advanced
medical imaging technique providing rich information about
the human soft tissue anatomy. The goal of brain MRI
segmentation is to accurately identify the principal tissue
structures in these image volumes. There are many methods
that exist to segment the brain. ne of these! conventional
methods that use pure image processing techniques are not
preferred because they need human interaction for accurate
and reliable segmentation. "nsupervised methods! on the other
hand! do not require any human interference and can segment
the brain #ith high precision. In the light to this fact! $ novel
approach is developed. ur approach is based on intensity
based thresholding to get boundaries bet#een cerebrospinal
fluid (%&')! (ray Matter ((M)! )hite Matter ()M) and
others. $fter the brain extraction by mathematical morphology
algorithm! #e proceed to brain segmentation. The %&' is
segmented by using orthogonal polynomial transform. 'inally
the gray matter and #hite matter regions in the MRI are
segmented based up on the intensity values. *xperimental
results sho# that the proposed method achieves reasonable
good segmentation.
Keywords- Brain segmentation, Magnetic resonance
imaging, skull stripping, Morphological operator, White Matter
(WM), Cerebrospinal luid(C!"), #hresholding, $ray matter
($M)
I. IN%"&DUC%I&N
'agnetic resonance imaging ('"I) is an important
diagnostic imaging techni*ue to obtain high *uality brain
images in both clinical and research areas because it is
virtually non invasive and it possesses a high spatial
resolution and an e+cellent contrast of soft tissues ,-., ,..
'" images are /idely used not only for detecting tissue
deformities such as cancers and injuries, but also for
monitoring patients /ith neurodegenerative diseases such as
0ar#inson1s disease, $l2heimer1s disease ($D), epilepsy,
schi2ophrenia and multiple sclerosis ('S) ,-. 3 ,4.. '"I is
also used for studying brain pathology. In order to offer
useful and accurate clinical information, the segmentation
and recognition algorithms of '" images are becoming
important subject of the study on medical image processing.
5rain tissue segmentation typically classifies vo+els into
grey matter (6'), /hite matter (7'), and Cerebrospinal
fluid (CS8). Segmentation of '" brain images into different
classes of tissue is an important tas# for improving the
understanding of many neurological disorders.
'ost '"I segmentation techni*ues can be categori2ed
into automatic and semi9automatic methods ,:., ,-;..
Segmentation of '"I is performed manually by trained
radiologists, but no/ there are many recent developments are
employing to segment the '"I, since manual segmentation
of images is a time consuming process and is susceptible to
human errors. So there is a need for computer analysis of
'"I such as precise delineation of tumours and reliable
reproducible segmentation of images.
In segmenting '"I data, /e have mainly three
considerable difficulties< noise, partial volume effects (/here
more than one tissue is inside a pi+el volume) and intensity
in9homogeneity ,-.. %he majority of intensity in9
homogeneities are caused by the irregularities of the scanner
magnetic fields3static (5=), radio9fre*uency (5-) and
gradient fields, /hich produce spatial changes in tissue
static. 0artial volume effects occur /here multiple tissues
contribute to a single vo+el, ma#ing the distinction bet/een
tissues along boundaries more difficult. Noise in '" images
can induce segmentation regions to become disconnection.
%/o main reasons lead to the problem of partial volume
effects. &n the one hand, due to the imaging resolution, the
comple+ity of tissue boundaries causes many vo+els to be
composed of at least t/o or more tissues. &n the other hand,
the constitution of a brain cannot be restricted to only three
pure tissues (6', 7', and CS8). %herefore, due to the
characteristics of brain '"I, development of automated
segmentation algorithms re*uire preprocessing /hich
includes denoising, striping of s#ull.
%his paper presents a ne/ segmentation method for
denoising and s#ull striping using a se*uence of
mathematical morphological operations< erosion and dilation
and their compositions i.e., opening and closing. %he
operators of morphological processing are particularly useful
for the analysis of binary images so that '"I images needed
to be previously binari2ed. $fter the s#ull striping process,
the cerebrospinal fluid is segmented by using orthogonal
polynomial transform ,-..
%herefore our present approach consists of t/o stages,
one is preprocessing and the second is segmentation. In the
first stage, the s#ull from the sample image is stripped and in
the second stage, the cerebrospinal fluid (CS8) region is
segmented from the s#ull stripped image using orthogonal
polynomial transform. 8inally the gray matter and /hite
matter regions are segmented from the s#ull stripped image
based on intensity values.
%he ne+t section presents some basics on morphological
operations. Section > describes our methodology for
stripping s#ull. Section ? describes the segmentation of grey
matter (6'), /hite matter (7'), and Cerebrospinal fluid
(CS8). %he e+perimental results for the proposed method are
demonstrated in section ; and finally dra/n some
conclusions and future /or# perspectives in section 4.
II. '$%@E'$%IC$A '&"0@&A&6B C&NCE0%S
'athematical morphology is a non9linear image analysis
techni*ue that e+tracts image objects information by
describing its geometrical structure in a formal /ay ,:..
'athematical morphology has been largely used in several
practical image processing and analysis problems ,C.. @ere
/e briefly revie/ some mathematical morphology operators
and the corresponding operations used in this /or#.
'athematical operators ta#e t/o data as an input< an
image to be processed and a structuring element, /hich is a
matri+ used for defining a neighbourhood shape and si2e ,-..
5y choosing the shape and si2e of the element, /e can
influence the morphological operations sensitivity to specific
shapes appearing in the processed image. %he elementary
shapes of symmetrical structuring elements ,-=. used in the
follo/ing processing are sho/n in 8ig. -.
%he erosion of binary image I by structuring element S is
defined by the formula ,-.<
{, :

} (1)
%he dilation of binary image I by structuring element S
is defined by the formula ,-.<
{, :

} (2)
Aet f < D "
n
" be an image function and g<6 "
n
"
be a structuring function. %he t/o fundamental operations of
gray9scale morphology, erosion and dilation are defined as<
Definition -< ,D. (Dilation) %he dilation of the function
f(+) by the structuring function g(+), (f g)(+), is given by<
(f g)(+) E ma+Ff(2) G (g+)(2) < 2 D,g+.H (>)
Definition < ,D. (Erosion) %he erosion of the function
f(+) by the structuring function g(+), (f g)(+), is given by<
(f g)(+) E minFf(2) I (g+)(2) < 2 D,g+.H (?)
/here g+ indicates the translation by + (g+)(2) E g(2 I +),
and D,g+. denotes the domain of the translated structuring
function. %he operations of closing and opening are the
combinations of erosion and dilation, both using the same
structuring element. 'orphological opening is erosion
follo/ed by dilation and morphological closing is dilation
follo/ed by erosion. %he 8ig.> sho/s that in a binari2ed
image there are some remaining pi+els that represent the
noise. %o remove the left9over pi+els the opening operation
/as used.

(a) (b)
8igure -. Dis# shape structuring elements< (a) 9pi+el radius, (b) ;9pi+el
radius
III. 0"&0&SED 'E%@&D&A&6B 8&" S%"I00IN6 SJUAA %&
SE6'EN% 5"$IN
%his section presents the proposed methodology for
segmenting brain '"I images. %he fundamental tas# in
brain '"I segmentation is the classification of volumetric
data into grey matter, /hite matter and cerebrospinal fluid
but it is not easy as there are some inherent difficulties
associated /ith image segmentationK among them are "8
coil in homogeneity, brain tissue susceptibility and other
systematic artifacts. Larious preprocessing steps have been
proposed to deal /ith some or all of these difficulties. S#ull
stripping is the first processing step in the segmentation of
brain tissue as sho/n in 8ig. .
8igure . &vervie/ of proposed methodology
In the proposed method for s#ull stripping, /e see the
brain surface as a smooth manifold /ith relatively lo/
curvature that separates brain from non9brain regions. $lso,
the brain corte+ can be visuali2ed as a distinct dar# ring
surrounding the brain tissues in the %-9/eighted a+ial '"
images.
%he steps involved in the proposed methodology for s#ull
stripping consists of three steps.
step-< 5inari2ation of every image.
step< &pening operation and closing operation on every
image in the se*uence using the structuring element.
step>< $pplying the binary mas# to the received '"I
input image.
A. Binarization
5inari2ation is the process that converts a grey level
image into a binary image. %he binari2ation process involves
e+amining the grey9level value of each pi+el in the enhanced
image, and if the value is greater than the global threshold,
then the pi+el value is set to a binary value oneK other/ise it
is set to 2ero.
(a) (b)
8igure >. (a) Input Image, (b) 5inari2ed Image
B. Morphological Operation
%he binary morphological operators are then applied on
the binari2ed image. Elimination of any obstacles and noise
from the image is the primary function of the morphological
operators ,C.. %he morphological operators namely, opening
and closing are being employed in the proposed method.
1) Opening: $n opening operation consists of erosion
follo/ed by dilation /ith the same structuring element.
&pening operator consists of an erosion follo/ed by a
dilation and can be used to eliminate all pi+els in regions
that are too small to contain the structuring element. In this
case the structuring element is often called a probe, because
it is probing the image loo#ing for small objects to filter out
the image ,--..
%he morphological opening of I by S, denoted as IS is
simply erosion of I by S, follo/ed by dilation of the result
by S ,--..
IS E (I S) S (;)
8igure ?. 5inari2ed image after applying opening operator
%he 8ig. ? sho/s the image after applying the opening
operator. 'orphological opening removes completely
regions of an object that cannot contain the structuring
element, smoothens object contours, brea#s thin connections
and removes this protrusion.
2) Closing: $ closing operation consists of a dilation
follo/ed by erosion /ith the same structuring element. %he
morphological closing of I by S, denoted as IS ,--.,
IS E (I S) S (4)
Ai#e opening, morphological closing operator tends to
smooth the contours of objects, it joins narro/ brea#s, fills
holes smaller than the structuring element. %he 8ig. ; sho/s
the image after applying the closing operator.
8igure ;. 5inari2ed image after applying closing operator
3) Erosion: Erosion operation on an image I containing
labels = and -, /ith a structuring element S, changes the
value of pi+el i in I from - to =, if the result of convolving S
/ith I, centered at i, is less than some predetermined value.
7e have set this value to be the area of S, /hich is basically
the number of pi+els that are - in the structuring element
itself. %he structuring element (also #no/n as the erosion
#ernel) determines the details of ho/ particular erosion
thins boundaries.
4) Dilation: Dual to erosion, a dilation operation on an
image I containing labels = and -, /ith a structuring element
S, changes the value of pi+el i in I from = to -, if the result
of convolving S /ith I , centered at i , is more than some
predetermined value. 7e have set this value to be 2ero. %he
structuring element (also #no/n as the dilation #ernel)
determines the details of ho/ a particular dilation gro/s
boundaries in an image
8igure 4. 5rain 'as#
C. Region-ase! inar" #as$ e%traction
"egion9based e+traction is done by e+amining the
properties of each bloc# that satisfy some criteria. 7e have
used one of t/o criteria. &ne criterion is to loo# at the ma+9
min difference and the other is to determine the mean values
of the bloc#s. %he process results /ith a brain mas# as
sho/n in 8ig.4 is then applied to the original '"I image as
sho/n in 8ig. -. Conse*uently, /e attain a brain '"I image
/ith its brain corte+ stripped as sho/n in 8ig. :.
8igure :. S#ull Stripped 5rain Image
IL. SE6'EN%$%I&N &8 CS8, 6' $ND 7'
A. &eg#entation o' cererospinal 'l(i!
"egarding CS8 segmentation, /e assume that there
e+ists some contrast bet/een brain tissue (gray matter and
/hite matter) and cerebrospinal fluid, /hich separates the
brain from the e+tra9cranial tissue. %he segmentation
methods /e have seen so far can be roughly grouped into
categories< intensity based or surface based. &ur method is
an intensity based method and it does simple thresholding.
In order to segment the cerebrospinal fluid from the brain
'"I image, /e apply the orthogonal polynomial transform
to the s#ull stripped image. 0rior to transformation, the
image S is blended using the formula,
( ) M) (M N =; . =
-==
O

>
) (
& ran!
&
&in &
i
+

,
_

(:)
1) Orthogonal pol"no#ial trans'or#: Aet
) = M ( l p
l
be
a se*uence of orthogonal polynomials on
)
/ith respect to
some /eight function
) (% *
, and let
l

be defined ,-, ->..

Aet
l

be the leading coefficient of

l
p
. 7e choose a value
= #
, and define
) P(
- -

# # # #
c
. %hen the follo/ing
e*uation holds ,-?.
( )

'

<

" % % p % p % p % p c
" %
" %
% p " p % p " p
c
" p % p
# # # # #
# # # #
#
l l
# l
l
, ) ( O ) ( ) ( O ) (
,
) ( ) ( ) ( ) (
) ( ) (
-
- -
- -
=

(D)
7here
l
pO denotes the derivative of
l
p .$fter applying
the polynomial transform, the region corresponding to the
CS8 are segmented as in the 8ig. D.
8igure D. Segmented cerebrospinal 8luid
B. +hite #atter an! ,ra" #atter seg#entation
8ollo/ing CS8 segmentation, the ne+t step is the
segmentation of /hite matter and grey matter present in the
brain '"I. %he input to the process is the s#ull stripped
image. %he major steps used to segment the gray matter and
/hite matter is as sho/n in 8ig C belo/.
8igure C. Steps to segment 6' and 7'
%he s#ull stripped input image & is smoothened by
applying the 9d 6aussian convolution filter to obtain
another image as sho/n in 8ig.-=.
8igure -=. Smoothening "esults
%hen, the
%
,
"
gradients of the smoothened image is
computed (8ig ?). %he gradient of t/o variables
%
and
"

is defined by,

-
"
'
i
%
'
" % ' ) , (
(C)
8igure --. (a) 6radient /.r.to + (b) 6radient /.r.to y
Using the gradient values, the edges present in the image
are mar#ed using the follo/ing e*uations,

) (

) ( i i
" % . +
(-=)
.
E
)
+

-
-
(--)
%he image
)
E
/ith the edges mar#ed, is then
subjected to binari2ation. %he binari2ation process involves
e+amining the grey9level value of each pi+el in the enhanced
image by means of global threshold / . %he global
threshold / is determined by means of the function,
) (
) /h
E , /
(-)
%hen the binari2ed image B) is subjected to binary
morphological operators opening and closing. %he
morphological operators are applied mainly for the purpose
of removing any of the obstacles and noise from the image.
%he /hite matter +M and the gray matter ,M
tissues in the brain '"I are finally segmented (thresholding)
based on their intensity values
8igure -. (a) segmented 6' (b) segmented 7'
L. EQ0E"I'EN%$A "ESUA%S
%he e+perimental results of the proposed methodology
for segmenting cerebrospinal fluid (CS8), gray matter (6'),
/hite matter (7') of '"I brain images are presented in
this section. %he proposed methodology is implemented in
'atlab (:.?). %he input to the proposed methodology is %-9
/eighted brain '"I images collected from publicly
available databases (http<PP///.bic.mni.mcgill.caPbrain/eb)
%he proposed methodology is based on Intensity
%hresholding (I%), /hich is the easiest and fastest
segmentation method, often adopted for preprocessing of
medical images and preregistration problems. %he sample
results of brain '"I segmentation obtained using the
proposed methodology is sho/n in the follo/ing figures.

(a) (b)
) -> (
= K
- K

'

i
i
o(t
B) ,M
B) +M
R

(c)
(d) (e)
8igure ->. (a) Input Image, (b) Segmented 5rain Image (c) CS8
Segmented Image (d) segmented 6' (e) segmented 7'
(a) (b)
(c)
(d) (e)
8igure -?. (a) Input Image, (b) Segmented 5rain Image (c) CS8
Segmented Image (d) segmented 6' (e) segmented 7'
LI. C&NCAUSI&N
In this paper, an automated, simple and efficient brain
'"I segmentation method for segmenting cerebrospinal
fluid (CS8) has been presented. Initially, the corte+ present
in the brain '"I images is e+tracted by combining
preprocessing techni*ues and incorporating mathematical
morphological operators and later cerebrospinal fluid is
segmented using orthogonal polynomial transform (&0%).
E+perimental results have sho/ed that the proposed method
does a reasonably good job in terms of segmenting s#ull and
CS8. In this present paper normal images /ere used. So, in
future, the method can be implemented on the abnormal
images.
$CJN&7AED6'EN%
7e than# Dr.0.Chinnadurai, Secretary R Correspondent,
0animalar Engineering college, Chennai, India for providing
support and facilities to do this research /or# and 5ernard
Institute of "adiology for providing the '" images.
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